Spatial co-expression and cell-cell communication inference from spatially resolved transcriptomics with CONCISE

Abstract

Cell-cell communication is fundamental to tissue organization, homeostasis, and disease progression. Recent advances in spatial transcriptomics provide unprecedented opportunities to systematically characterize ligand-receptor interactions directly within intact tissues. However, robust inference of spatial ligand-receptor interactions remains challenging because intrinsic features of spatial transcriptomics data, including spatial autocorrelation, variation in total molecular counts, and measurement errors, can induce spurious spatial co-expression and lead to inflated false-positive results. Most existing methods do not adequately account for these confounding factors, limiting the reliability of inferred cellular communication. Here, we present CONCISE, a statistical method for spatially constrained co-expression and ligand-receptor interaction inference that jointly models spatial autocorrelation, variation in total molecular counts, measurement errors, and spatial proximity constraints. CONCISE combines efficient moment-based parameter estimation with analytical hypothesis testing, enabling fast and statistically rigorous inference without restrictive distributional assumptions. Through extensive simulations, real-data permutation experiments, and biologically motivated negative-control analyses across different spatial transcriptomics platforms, we show that most existing methods presented inflated false-positive rates, whereas CONCISE achieved well-calibrated inference, robust false-positive control, and improved detection power. Application of CONCISE to high-resolution MERFISH and CosMx datasets from intestinal inflammation and non-small cell lung cancer further highlights its biological utility in disease contexts. CONCISE uncovered inflammation-associated fibroblast-specific interactions during intestinal inflammation and delineated complex tumor-immune and tumor-stromal signaling networks within the tumor microenvironment.